Pre‐built Database Indexes

This page contains links to databases that are pre-formatted for use with Lambda (so that you don't have to index them yourself). If you have created indexes yourself and would like to share them, you can send us a link.

lambda3 branch

• Unpacking the file after download is not required; you can use it as-is. However, unzipped files may load slightly faster during search (this depends on disk vs CPU speed).
• Taxonomy information is included in some indexes, see Taxonomic Workflows for more information.
• Memory usage during search is usually Unpacked Size + size-of-query-file ± 10%. The memory usage during the creation of the indexes was higher, around 10x input size.

Protein databases

Database	Log	Date	Tax	Download Size
⇩ Uniref90	📄 Log	20230713	☑	145GB
⇩ Uniref50	📄 Log	20230713	☑	44GB
⇩ Uniprot Sprot	📄 Log	20230713	☑	0.4GB

Databases used in the paper

Database	Date	Tax	Download Size	Domain
⇩ Uniref50	20220525	☐	38GB	Protein
⇩ Human microbiome project	20220607	☐	12GB	Nucleotide
⇩ Human microbiome project	20220607	☐	20GB	Bisulfite
⇩ Human microbiome project (+ mm10 + hg19)	20220607	☐	39GB	Bisulfite
⇩ Fungi genomes	20220607	☐	15GB	Bisulfite

lambda2 branch (1.9.3 - 2.0.1)

• Unpack the file after download with tar xf FILE.lambda.tar.gz. The resulting .lambda directory is the index.
• Taxonomy information is included in some of the indexes, see Taxonomic Workflows for more information.
• Memory usage during search is usually Unpacked Size + size-of-query-file ± 10%. The memory usage during the creation of the indexes was higher, around 2.5 * Unpacked Size.

Database	Date	Tax	Download Size	Unpacked Size
⇩ NR	20171205	☑	79GB	151GB
⇩ Uniref100	20171205	☐	75GB	137GB
⇩ Uniref90	20171205	☐	40GB	64GB
⇩ Uniref50	20171205	☐	16GB	25GB
⇩ Uniprot Trembl	20171205	☐	54GB	98GB
⇩ Uniprot Sprot	20171205	☑	0.3GB	0.7GB